FMO DATABASE

FMODB ID: R57Q8

Calculation Name: 3R84-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R84

Chain ID: A

ChEMBL ID:

UniProt ID: Q99278

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-494745.40787
FMO2-HF: Nuclear repulsion	461638.921414
FMO2-HF: Total energy	-33106.486457
FMO2-MP2: Total energy	-33203.650117

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)

Summations of interaction energy for fragment #1(A:4:GLY)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-0.629	2.729	5.762	-4.31	-4.81	-0.012

Interaction energy analysis for fragmet #1(A:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.095 / q_NPA : 0.040

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	6	ILE	0	0.069	0.020	3.576	-1.032	0.798	0.003	-0.975	-0.858	0.005
4	A	7	GLN	0	0.033	0.022	2.062	-2.490	-1.975	5.756	-2.964	-3.307	-0.016
5	A	8	GLU	-1	-0.871	-0.927	3.696	-4.383	-3.449	0.004	-0.365	-0.573	-0.001
6	A	9	ARG	1	0.799	0.890	5.841	2.887	2.887	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.018	0.006	7.280	0.408	0.408	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.910	0.951	4.200	3.682	3.761	-0.001	-0.006	-0.072	0.000
9	A	12	SER	0	-0.058	-0.039	9.469	0.346	0.346	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.010	-0.010	11.693	0.208	0.208	0.000	0.000	0.000	0.000
11	A	14	ASN	0	-0.038	-0.030	11.683	0.009	0.009	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.899	-0.952	13.579	-0.522	-0.522	0.000	0.000	0.000	0.000
13	A	16	ILE	0	-0.003	-0.011	15.422	0.107	0.107	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.859	-0.925	16.209	-0.480	-0.480	0.000	0.000	0.000	0.000
15	A	18	THR	0	-0.001	0.011	17.527	0.076	0.076	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.081	-0.054	17.979	0.100	0.100	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.023	0.009	21.372	0.043	0.043	0.000	0.000	0.000	0.000
18	A	21	CYS	0	-0.011	-0.002	22.307	0.039	0.039	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.042	-0.023	23.862	0.032	0.032	0.000	0.000	0.000	0.000
20	A	23	MET	0	-0.030	0.003	25.987	0.014	0.014	0.000	0.000	0.000	0.000
21	A	24	LEU	0	0.020	0.013	26.892	0.020	0.020	0.000	0.000	0.000	0.000
22	A	25	GLN	0	0.034	0.014	28.156	0.021	0.021	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.841	-0.909	29.800	-0.165	-0.165	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.035	0.029	32.114	0.013	0.013	0.000	0.000	0.000	0.000
25	A	28	SER	0	-0.004	0.015	33.148	0.013	0.013	0.000	0.000	0.000	0.000
26	A	29	GLN	0	-0.039	-0.025	32.374	0.017	0.017	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.005	0.009	36.110	0.009	0.009	0.000	0.000	0.000	0.000
28	A	31	THR	0	-0.030	-0.033	37.761	0.008	0.008	0.000	0.000	0.000	0.000
29	A	32	PHE	0	-0.003	-0.009	39.467	0.006	0.006	0.000	0.000	0.000	0.000
30	A	33	ILE	0	-0.004	-0.011	38.925	0.005	0.005	0.000	0.000	0.000	0.000
31	A	34	PHE	0	0.006	0.007	42.340	0.006	0.006	0.000	0.000	0.000	0.000
32	A	35	GLY	0	0.002	-0.001	44.325	0.005	0.005	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.839	-0.910	44.854	-0.069	-0.069	0.000	0.000	0.000	0.000
34	A	37	LEU	0	-0.007	-0.002	44.762	0.004	0.004	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.888	0.958	48.319	0.077	0.077	0.000	0.000	0.000	0.000
36	A	39	ARG	1	0.843	0.916	48.900	0.069	0.069	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.012	0.014	51.759	0.003	0.003	0.000	0.000	0.000	0.000
38	A	41	ASN	0	-0.045	0.000	47.306	0.003	0.003	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.829	-0.936	48.370	-0.078	-0.078	0.000	0.000	0.000	0.000
40	A	43	SER	0	-0.081	-0.058	47.629	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	44	VAL	0	0.000	0.003	42.980	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.936	0.984	43.022	0.077	0.077	0.000	0.000	0.000	0.000
43	A	46	PRO	0	0.057	0.013	42.361	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.050	0.016	38.966	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	48	PHE	0	-0.030	-0.005	38.352	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.889	-0.951	38.927	-0.104	-0.104	0.000	0.000	0.000	0.000
47	A	50	ASN	0	-0.079	-0.047	33.783	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	51	HIS	1	0.853	0.896	33.304	0.135	0.135	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.031	0.030	34.047	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.934	0.974	33.502	0.135	0.135	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.027	0.018	29.338	0.001	0.001	0.000	0.000	0.000	0.000
52	A	55	PHE	0	-0.014	-0.001	29.672	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	56	TYR	0	0.016	0.012	29.985	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.902	-0.962	28.202	-0.203	-0.203	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.867	0.934	24.703	0.224	0.224	0.000	0.000	0.000	0.000
56	A	59	LEU	0	0.020	0.013	25.257	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.908	-0.937	26.297	-0.279	-0.279	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.961	0.988	19.523	0.400	0.400	0.000	0.000	0.000	0.000
59	A	62	SER	0	-0.008	-0.014	21.146	-0.038	-0.038	0.000	0.000	0.000	0.000
60	A	63	THR	0	-0.038	-0.035	21.340	-0.037	-0.037	0.000	0.000	0.000	0.000
61	A	64	THR	0	0.011	0.012	21.468	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.065	-0.029	14.850	0.068	0.068	0.000	0.000	0.000	0.000
63	A	66	LEU	0	0.019	-0.006	17.840	-0.068	-0.068	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.916	0.964	19.322	0.374	0.374	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.930	0.961	13.318	0.880	0.880	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.752	-0.850	12.964	-1.252	-1.252	0.000	0.000	0.000	0.000
67	A	70	ILE	0	0.006	0.011	15.672	-0.024	-0.024	0.000	0.000	0.000	0.000
68	A	71	GLN	0	0.009	0.025	18.140	0.014	0.014	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.019	-0.014	12.022	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.028	0.001	13.797	-0.032	-0.032	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.892	-0.947	15.293	-0.295	-0.295	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.949	-0.974	15.415	-0.476	-0.476	0.000	0.000	0.000	0.000
73	A	76	ASN	0	-0.099	-0.085	10.984	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	77	VAL	0	0.044	0.035	14.058	0.022	0.022	0.000	0.000	0.000	0.000
75	A	78	GLY	0	-0.028	-0.011	16.429	0.026	0.026	0.000	0.000	0.000	0.000
76	A	79	THR	0	-0.045	-0.016	12.977	0.013	0.013	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.875	0.938	6.854	0.931	0.931	0.000	0.000	0.000	0.000
78	A	81	LEU	0	-0.034	-0.007	10.904	0.001	0.001	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.004	0.004	13.547	0.048	0.048	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.040	0.017	16.693	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	84	ILE	0	-0.017	0.006	19.914	0.012	0.012	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)